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Gaussian 03 is the latest in the Gaussian series of electronic structure programs. Gaussian 03 is used by chemists, chemical engineers, biochemists, physicists and others for research in established and emerging areas of chemical interest.
Starting from the basic laws of quantum mechanics, Gaussian predicts the energies, molecular structures, and vibrational frequencies of molecular systems, along with numerous molecular properties derived from these basic computation types. It can be used to study molecules and reactions under a wide range of conditions, including both stable species and compounds which are difficult or impossible to observe experimentally such as short-lived intermediates and transition structures. This article introduces several of its new and enhanced features.
Investigating the Reactivity and Spectra of Large Molecules
Traditionally, proteins and other large biological molecules have been out of the reach of electronic structure methods. However, Gaussian 03’s ONIOM method overcomes these limitations. ONIOM first appeared in Gaussian 98, and several significant innovations in Gaussian 03 make it applicable to much larger molecules.
This computational technique models large molecules by defining two or three layers within the structure that are treated at different levels of accuracy. Calibration studies have demonstrated that the resulting predictions are essentially equivalent to those that would be produced by the high accuracy method.
The ONIOM facility in Gaussian 03 provides substantial performance gains for geometry optimizations via a quadratic coupled algorithm and the use of micro-iterations. In addition, the program’s option to include electronic embedding within ONIOM calculations enables both the steric and electrostatic properties of the entire molecule to be taken into account when modeling processes in the high accuracy layer (e.g., an enzyme’s active site). These techniques yield molecular structures and properties results that are in very good agreement with experiment.
For example, researchers are currently studying excited states of bacteriorhodopsin (illustrated below) using an ONIOM(MO:MM) model, as a first step in understanding the means by which this species generates energy within a cell. In this two-layer approach, the active site is treated using an electronic structure method while the rest of the system is modeled with molecular mechanics. Electronic embedding, which includes the electrostatics of the protein environment within the QM calculation of the active site, is essential to accurate predictions of the molecule’s UV-Visible spectrum.
The ONIOM method is also applicable to large molecules in many other areas, including enzyme reactions, reaction mechanisms for organic systems, cluster models of surfaces and surface reactions, photochemical processes of organic species, substituent effects and reactivity of organic and organometallic compounds, and homogeneous catalysis.
Other new ONIOM related features in Gaussian 03:
| • | Customizable molecular mechanics force fields. |
| • | Efficient ONIOM frequency calculations. |
| • | ONIOM calculation of electric and magnetic properties. |
Determining Conformations via Spin-Spin Coupling Constants
Conformational analysis is a difficult problem when studying new compounds for which X-ray structures are not available. Magnetic shielding data in NMR spectra provides information about the connectivity between the various atoms within a molecule. Spin-spin coupling constants can aid in identifying specific conformations of molecules because they depend on the torsion angles with the molecular structure.
Gaussian 03 can predict spin-spin coupling constants in addition to the NMR shielding and chemical shifts available previously. Computing these constants for different conformations and then comparing predicted and observed spectra makes it possible to identify the specific conformations that were observed. In addition, the assignment of observed peaks to specific atoms is greatly facilitated.
Studying Periodic Systems
Gaussian 03 expands the range of chemical systems that it can model to periodic systems such as polymers and crystals via its periodic boundary conditions (PBC) methods. The PBC technique models these systems as repeating unit cells in order to determine the structure and bulk properties of the compound.
For example, Gaussian 03 can predict the equilibrium geometries and transition structures of polymers. It can also study polymer reactivity by predicting isomerization energies, reaction energetics, and so on, allowing the decomposition, degradation, and combustion of materials to be studied. Gaussian 03 can also model compounds’ band gaps.
Other PBC capabilities in Gaussian 03:
| • | 2D PBC methods can be used to model surface chemistry, such as reactions on surfaces and catalysis. In addition, using Gaussian 03 allows you to study the same problem using a surface model and/or a cluster model, using the same basis set and Hartree-Fock or DFT theoretical method in both cases. Using Gaussian 03 enables you to choose the appropriate approach for the system you are studying, rather than being forced to frame the problem to fit the capabilities and limitations of a particular model. |
| • | 3D PBC: The structures and available bulk properties of crystals and other three-dimensional periodic systems can be predicted. |
Predicting Spectra
Gaussian 03 can compute a very wide range of spectra and spectroscopic properties. These include:
| • | IR and Raman |
| • | Pre-resonance Raman |
| • | UV-Visible |
| • | NMR |
| • | Vibrational circular dichroism (VCD) |
| • | Electronic circular dichroism (ECD) |
| • | Optical rotary dispersion (ORD) |
| • | Harmonic vibration-rotation coupling |
| • | Anharmonic vibration and vibration-rotation coupling |
| • | g tensors and other hyperfine spectra tensors |
For example, Gaussian 03 computes many of the tensors which contribute to hyperfine spectra. These results are useful for making spectral assignments for observed peaks, something which is usually difficult to determine solely from the experimental data (see the example below). Using theoretical predictions to aid in interpreting and fitting observed results should make non-linear molecules as amenable to study as linear ones.
Modeling Solvent Effects on Reactions and Molecular Properties
Molecular properties and chemical reactions often vary considerably between the gas phase and in solution. For example, low lying conformations can have quite different energies in the gas phase and in solution (and in different solvents), conformation equilibria can differ, and reactions can take significantly different paths.
Gaussian 03 offers the Polarizable Continuum Model (PCM) for modeling system in solution. This approach represents the solvent as a polarizable continuum and places the solute in a cavity within the solvent.
The PCM facility in Gaussian 03 includes many enhancement that significantly extend the range of problems which can be studied:
| • | Excitation energies and related properties of excited states can be calculated in the presence of a solvent (see the surfaces at the upper right). |
| • | NMR spectra and other magnetic properties. |
| • | Vibrational frequencies, IR and Raman spectra, and other properties computed via analytic second derivatives of the energy. |
| • | Polarizabilities and hyperpolarizabilities. |
| • | General performance improvements. |
Software chimica
Programma chimica
Programma struttura elettronica
Meccanica quantistica
Struttura molecolare
Proprieta molecolare
Spettroscopia nmr
Proprieta magnetiche
Dinamica molecolare
The small surface at the top right shows the electron density difference in the gas phase, and the one to its left shows the difference in acetonitrile solution. Electron density moves from the green areas to the red areas in the excited state.
The larger surface below the small ones is the difference of these difference densities (solution minus gas phase), and it illustrates how the charge transfer from NH2 to NO2 from the ground state to the excited state
In addition, as the level diagrams indicate, the ordering of the lowest two excited states changes between the gas phase and in solution with acetonitrile (the yellow states have 0 oscillator strengths and are not observed in ordinary UV-Visible spectra).
Gaussian 03W can be used to model many properties:
| • | Energies using a wide variety of methods, including Hartree-Fock, Density Functional Theory, MP2, Coupled Cluster, and high accuracy methods like G3, CBS-QB3 and W1U. |
| • | Geometries of equilibrium structures and transition states (optimized in redundant internal coordinates for speed), including QST2 transition structure searching. |
| • | Vibrational spectra, including IR, non-resonant and pre-resonance Raman intensities, anharmonic vibrational analysis and vibration-rotation coupling. |
| • | Magnetic properties, including NMR chem-ical shifts and spin-spin coupling constants. |
| • | Spectra of chiral molecules: optical rotations, VCD and ROA. |
| • | G tensors and other contributions to hyper-fine spectra. |
Gaussian 03W can study compounds and reactions under a wide range of conditions:
| • | In the gas phase and in solution. |
| • | In the solid state, using the Periodic Boundary Conditions facility. |
| • | Excited states can be studied with several methods: CASSCF and RASSCF, Time Dependent DFT and SAC-CI. |
| • | The Atom Centered Density Matrix Propagation (ADMP) method can be used to perform molecular dynamics simulations in order to study reaction paths and product state distributions. |
Gaussian 03M can be used to model many properties:
| • | Energies using a wide variety of methods, including Hartree-Fock, Density Functional Theory, MP2, Coupled Cluster, and high accuracy methods like G3, CBS-QB3 and W1U. |
| • | Geometries of equilibrium structures and transition states (optimized in redundant internal coordinates for speed), including QST2 transition structure searching. |
| • | Vibrational spectra, including IR, non-resonant and pre-resonance Raman intensities, anharmonic vibrational analysis and vibration-rotation coupling. |
| • | Magnetic properties, including NMR chem-ical shifts and spin-spin coupling constants. |
| • | Spectra of chiral molecules: optical rotations, VCD and ROA. |
| • | G tensors and other contributions to hyperfine spectra. |
Gaussian 03M can study compounds and reactions under a wide range of conditions:
| • | In the gas phase and in solution. |
| • | In the solid state, using the Periodic Boundary Conditions facility. |
| • | Excited states can be studied with several methods: CASSCF and RASSCF, Time Dependent DFT and SAC-CI. |
| • | The Atom Centered Density Matrix Propagation (ADMP) method can be used to perform molecular dynamics simulations in order to study reaction paths and product state distributions. |
New Chemistry
Enhanced ONIOM Method
The ONIOM facility in Gaussian 03 has been significantly enhanced over that offered by Gaussian 98 [1-2]:
| • | The ONIOM facility [42] now supports electronic embedding for ONIOM(MO:MM) calculations: the electrostatic properties of the MM region can be taken into account during computations on the QM region. | ||||
| • | ONIOM(MO:MM) optimizations are much faster and can be reliably performed for large molecules (e.g., proteins). The algorithmic improvements include:
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| • | Analytic frequencies are available for ONIOM(MO:MM) calculations, and frequencies for ONIOM(MO:MO) calculations are significantly faster. | ||||
| • | Gaussian 03 provides support for general molecular mechanics (MM) force fields, including read-in and modified parameters. A standalone MM optimization program is also included. | ||||
| • | Support for an external program for any ONIOM model (e.g., an external MM program may be used). |
Solvent Effects
The Polarizable Continuum Model (PCM) solvation method has been improved and extended [3-8]:
| • | The IEFPCM model [3,9] is now the default, and analytic frequencies are now available for this SCRF method. Additional performance improvements include a new cavity generation technique [10]. |
| • | Many additional properties can be modeled in solution (discussed later in this brochure). |
| • | Gaussian 03 can also produce input for Klamt's COSMO-RS program [11], which computes solvation energies, partition coefficients, vapor pressure and other bulk properties via statistical mechanics techniques. |
Periodic Boundary Conditions (PBC)
Gaussian 03 offers PBC calculations for studying periodic systems: e.g., polymers, surfaces and crystals [12-15]. PBC calculations solve the Schrödinger equation subject to the boundary condition that the molecule and the wavefunction repeat indefinitely in one, two or three directions. Hartree-Fock and DFT energies and gradients are available for periodic systems.
Molecular Dynamics
Dynamics calculations can provide qualitative understanding of reaction mechanisms and quantitative details about the reaction such as product distributions. There are two main approaches to performing these calculations:
| • | In Born-Oppenheimer Molecular Dynamics (BOMD), classical trajectories are calculated on a local quadratic approximation to the potential energy surface (for a review, see [16]). Our implementation [17] uses a Hessian-based algorithm for the predictor and corrector steps, an approach which results in a factor of 10 or more improvement in the step size over previous implementations. While it can make use of analytic second derivatives, BOMD is available for all theoretical methods having analytic gradients. |
| • | Gaussian 03 also offers Atom-Centered Density Matrix Propagation (ADMP) method [18-20] molecular dynamics (available for Hartree-Fock and DFT). Drawing on the work of Car and Parrinello [21], ADMP propagates the electronic degrees of freedom rather than solving the SCF equations at each nuclear geometry. Unlike CP, ADMP propagates the density matrix rather than the MOs. This is much more efficient if an atom-centered basis set is being used. This approach overcomes some limitations inherent in the CP implementation: e.g., there is no need to substitute D for H in order to maintain energy conservation, and both pure and hybrid DFT functionals can be used. ADMP calculations can also be performed in the presence of a solvent [22], and ADMP can be used in ONIOM(MO:MM) calculations. |
Excited States
There are additions and several enhancements to excited states methods:
| • | CASSCF calculations are now more efficient due to a new algorithm for evaluating the CI-vector in the full configuration interaction calculation [23]. Practical active spaces increase to about 14 orbitals for energies and gradients (they remain at about 8 orbitals for frequencies). |
| • | The Restricted Active Space (RAS) SCF method [24] is also available[25]. RASSCF calculations partition the molecular orbitals into five sections: the lowest lying occupieds (considered inactive in the calculation), the RAS1 space of doubly occupied MOs, the RAS2 space containing the most important orbitals for the problem, the RAS3 space of weakly occupied MOs and the remaining unoccupied orbitals (also treated as frozen by the calculation). Thus, the active space in CASSCF calculations is divided into three parts in a RAS calculations, and allowed configurations are defined by specifying the minimum number of electrons that must be present in the RAS1 space and the maximum number that must be in the RAS3 space, in addition to the total number of electrons in the three RAS spaces. |
| • | NBO orbitals for may be used for defining CAS and RAS active spaces. These provide good initial guesses for the required antibonding orbitals which correlate with the bonds/lone pairs of interest. |
| • | The Symmetry Adapted Cluster/Configuration Interaction (SAC-CI) method of Nakatsuji and coworkers is now included in Gaussian. This method has many uses: predicting very accurate excited states of organic systems, studying two-to-many electron excitation processes such as the shake-up in the ionization spectrum, and other problem types. For an overview of the SAC-CI method, see [26-27]. |
| • | Solvent Effects: Excited states can be modeled in the presence of a solvent [28-29] using the CI-Singles and Time Dependent Hartree-Fock and DFT methods. |
Molecular Properties
Gaussian 03 provides many new molecular properties:
| • | Spin-spin coupling constants [31-34], which can aid in distinguishing conformations in magnetic spectra. |
| • | g tensors and other hyperfine spectra tensors [49-52]. Gaussian 03 can produce nuclear electric quadrupole constants, rotational constants, the quartic centrifugal distortion terms, the electronic spin rotation terms, the nuclear spin rotation terms, the dipolar hyperfine terms and Fermi contact terms. All tensors can be exported to Pickett's fitting and spectral analysis program [53]. |
| • | Harmonic vibration-rotation coupling [43-44]: A spectroscopic property dependent on the coupling between molecules' vibrational and rotational modes. It is used to analyze detailed rotational spectra. |
| • | Anharmonic vibration and vibration-rotation coupling [44-48]: Using perturbation theory, these higher order terms are incorporated into frequency calculations in order to produce more accurate results. |
| • | Pre-resonance Raman spectra which yield information about ground state structures, connectivity, and vibrational states. |
| • | Optical Rotations/Optical Rotary Dispersion: Used to distinguish enantiomers of chiral systems [39-41] (this property is computed via GIAOs). |
| • | Electronic Circular Dichroism (ECD): This property is the differential absorption in the visible and ultraviolet regions for optically active molecules, and is used to assign absolute configurations [35-36]. Predicted spectra can also be useful in interpreting existing ECD data and peak assignments. |
| • | Frequency-dependent polarizabilities and hyperpolarizabilities, which can be used to study how the molecular properties of materials vary with wavelength of the incident light [37-38]. |
| • | Magnetic susceptibilities computed with Gauge-Independent Atomic Orbitals (GIAOs) [30]. This property is the magnetic analogue to the electric polarizability, and it provides insight into the diamagnetic vs. paramagnetic character of molecules. |
| • | Solvent Effects: Electric and magnetic properties and the various spectra can be predicted for systems in solution as well as ones in the gas phase [54-56]. |
| • | Properties with ONIOM: The ONIOM method may be used with these electric and magnetic properties. |
Fundamental Algorithms
| • | Much Better Initial Guesses: Gaussian 03 uses the Harris functional for generating initial guesses. This functional [59] is a non-iterative approximation to DFT, and it produces initial guesses which are better than those produced by Gaussian 98: for example, there are modest improvements for organic systems but very substantial improvements for compounds containing metals. |
| • | New SCF Convergence Algorithm: The default SCF algorithm now uses a combination of two Direct Inversion in the Iterative Subspace (DIIS) extrapolation methods EDIIS and CDIIS. EDIIS [58] uses energies for extrapolation, and it dominates the early iterations of the SCF convergence process. CDIIS, which performs extrapolation based on the commutators of the Fock and density matrices, handles the latter phases of SCF convergence. This new algorithm is very reliable, and previously troublesome SCF convergence cases now almost always converge with the default algorithm. For the few remaining pathological convergence cases, Gaussian 03 offers Fermi broadening and damping in combination with CDIIS (including automatic level shifting). |
| • | Density Fitting for Pure DFT Calculations: Gaussian 03 provides the density fitting approximation [60,61] for pure DFT calculations. This approach expands the density in a set of atom-centered functions when computing the Coulomb interaction instead of computing all of the two-electron integrals. It provides significant performance gains for pure DFT calculations on medium sized systems too small to take advantage of the linear scaling algorithms without a significant degradation in accuracy. Gaussian 03 can generate an appropriate fitting basis automatically from the AO basis, or you may select one of the built-in fitting sets. |
| • | Faster and Automated FMM: The fast multipole method (FMM) in Gaussian 98 allowed the computational cost for large DFT calculations to scale linearly with system size. In Gaussian 03, improvements to these algorithms [57] means that their performance gains can be realized for systems of more modest size as well (~100 atoms for pure DFT calculations and ~150 atoms with hybrid functionals). In addition, this feature is now fully automated: the program invokes FMM automatically when appropriate. |
| • | Coulomb Engine: Gaussian 03 incorporates a faster algorithm for the Coulomb operator for pure DFT calculations. The Coulomb engine produces the exact Coulomb matrix without explicitly forming four center two electron integrals. This substantially reduces the CPU time for the Coulomb problem in pure DFT calculations. |
| • | O(N) Exact Exchange: A new algorithm for Hartree-Fock and DFT calculations using hybrid functionals implements screening of the exact exchange contribution via the density matrix to eliminate the many zero value terms [62]. This technique results in a linear computational cost for these methods without accuracy loss. |
Additional Features
| • | Additional DFT Functionals:
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| • | High Accuracy Energy Methods:
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| • | Douglas-Kroll-Hess scalar relativistic Hamiltonian: This feature allows all electron calculations for heavier atoms (first and second transition rows) when ECPs are not accurate enough [63-66]. For an overview, see [67-68]. | ||||||||
| • | Gaussian 03 also includes the very large universal Gaussian basis set of de Castro, Jorge and coworkers [82], which approaches the basis set limit. |
TCP Linda is a parallel execution environment which has been used to create a parallel version of Gaussian for local area network and some distributed memory multiprocessor environments.
Supported workstations for TCP Linda parallel execution:
| • | IBM RS6000 (including the SP) running AIX 5.1 |
| • | Sun/Solaris 9 |
| • | HP Alpha/Tru64 |
| • | Intel Pentium III and IV and AMD Athlon/Duron (IA32) running Linux |
Shipping is extra for all books and manuals except for the student price for the Japanese translation of Exploring Chemistry. Note that book offerings change from time to time.
Title
| - | Gaussian 03 User's Reference and IOps Reference |
| - | Gaussian 03 Programmer's Reference |
| - | Gaussian 03 Pocket Reference |
| - | Exploring Chemistry with Electronic Structure Methods: Soft cover Student Hard cover Japanese translation (soft cover) Japanese translation student† price (includes shipping) |
| - | GaussView 3.0 User's Reference |
| - | Ab Initio Molecular Orbital Theory |
| - | Essential System Administration, 3rd Ed. |
| - | Learning GNU Emacs, 2nd Ed. |
| - | Learning the UNIX Operating System, 5th Ed. |
| - | Using csh and tcsh |
| - | TCP/IP Network Administration, 3rd Ed. |
| - | Learning Perl, 3rd Ed. |
| - | Programming Perl, 3rd Ed. |
| - | Advanced Perl Programming |